Truncated baff receptors

ABSTRACT

The disclosure provides a non-naturally occurring BAFF-R glycoprotein having a deletion in the extracellular domain which results in an altered 0-linked glycosylation pattern. The disclosure also provides methods and pharmaceutical compositions for treating B-cell- and T-cell-mediated disorders.

This application claims priority from U.S. Application Ser. No.60/458,707, filed Mar. 28, 2003, herein incorporated by reference in itsentirety.

FIELD OF THE INVENTION

The present disclosure relates to TNF-family ligands and receptors andantagonists and agonists thereof and their use in modulation of immuneresponses.

BACKGROUND OF THE INVENTION

The present invention relates to the BAFF receptor (“BAFF-R,” also knownas BR3 and Ztnfr12), a member of the TNF family of receptor proteins.BAFF-R has been described in International Patent Publication WO02/24909.

BAFF-R specifically binds the TNF family ligand, BAFF (also known asTALL-1, THANK, BLyS, neurokine α, TNSF13B, and zTNF4), which has beendescribed in International Patent Publication WO 00/43032. BAFF enhancesB cell survival in vitro (Batten et al. (2000) J. Exp. Med. 192(10):1453-1466) and has emerged as a key regulator of peripheral B cellpopulations in vivo. It is believed that abnormally high levels of thisligand may contribute to the pathogenesis of autoimmune diseases byenhancing the survival of autoreactive B cells (Batten et al., (2000) J.Exp. Med. 192(10): 1453-1466). Agonists and antagonists of BAFF activityhave been described in WO 00/43032.

Recently, BAFF-specific agents, including BAFF antibodies, have beendeveloped for treatment of autoimmune and other disorders (see, e.g.,U.S. patent application Ser. Nos. 09/911,777; 10/380,703; 10/045,574;and 60/512,880); Kalled et al., (2003) Expert Opin. Ther. Targets,7(1)115-23).

Prior to the discovery of BAFF-R, many members of the TNF receptorfamily had been uncovered by expressed sequence tag (EST) analysis andgenomic sequencing. However, some family members, like BAFF-R, requiredexpression cloning for their identification.

A member of the TNF receptor family, BAFF-R, is fairly divergent frommany family members. In particular, BAFF-R contains only onecysteine-rich domain with 4 cysteines, while most TNF receptor familymembers typically contain 2-4 domains, each with 6 cysteines. Thisabsence of a canonical receptor cysteine-rich domain preventedidentification of BAFF-R by sequence-based searches. It was also notclear exactly how BAFF-R achieves high-affinity binding to BAFF, andexactly what sequences are involved.

Not only is BAFF-R distinct from the canonical TNF receptor familymembers, human BAFF-R (hBAFF-R) is only 60% homologous with murineBAFF-R (mBAFF-R). This difference is reflected in the differentialaggregation of hBAFF-R (90% aggregated) and mBAFF-R (10% aggregated)when the extracellular domain is expressed in eukaryotic cells. However,two point mutations in hBAFF-R (V21N and L28P in SEQ ID NO:1) reduce itsaggregation to less than 10%. This mutated form of hBAFF-R is referredto as vBAFF-R.

TNF family members are known to possess both N-linked and O-linkedglycosylation sites. N-linked glycosylation occurs on asparagineresidues within distinct consensus sequences. O-linked glycosylationoccurs on serine and threonine residues, but a lack of sequence motifsand inconsistent addition of sugars within a population of proteinsprevents the prediction of the presence of O-linked glycans on aprotein. Additionally, O-linked glycosylation sites are often clusteredin short serine/threonine-rich sequences, making it difficult todetermine the exact number and location of the glycans. Even when apattern of glycosylation can be determined for a specific protein,O-linked glycosylation is tissue dependent, so the pattern varies withthe cell type in which the protein is being expressed.

The ability to analyze any given feature of a batch of protein productmay be important for producing polypeptides for pharmaceutical use. Theunpredictability and inconsistency of O-linked glycosylation leads todifficulties in manufacturing. For example, a large number of O-linkedglycans makes it unfeasible to characterize batches of proteinpharmaceuticals by mass spectrometry.

Possible solutions to this problem include the production of proteins inprokaryotic cells, which do not contain glycosylation machinery, and theproduction of proteins by chemical synthesis. However, glycosylatedproteins may have advantages over non-glycosylated proteins. Forexample, O-linked glycosylation aids in folding and maintaining tertiarystructure, causes increased stability and protease resistance, andmodulates interactions with other proteins. O-linked glycosylation mayalso influence a protein's biological activity. It is known that theactivity of many cell signaling molecules, including TNFα, is modulatedby the glycosylation of cell surface receptors (Van den Steen et al.(1998) Crit. Rev. Biochem. Mol. Biol. 33(3): 151-208). Additionally, theproduction of proteins by chemical synthesis for pharmaceutical use canbe prohibitively expensive.

Accordingly, a need exists to provide a BAFF-R protein for therapeuticuse with a glycosylation pattern that can be characterizedunambiguously, and that avoids aggregation in eukaryotic cells whilemaintaining specificity and affinity for BAFF.

SUMMARY OF THE INVENTION

The present invention is based, in part, on the discovery andcharacterization of the glycosylation pattern of human BAFF-R andvariants thereof. The invention is further based in part on thediscovery and demonstration that the extracellular domain (ECD) ofBAFF-R glycoprotein can be truncated without a substantial loss inligand binding despite the altered glycosylation pattern. The presentdisclosure provides a non-naturally occurring BAFF-R glycoprotein havinga deletion in the ECD that results in an altered O-linked glycosylationpattern. Such truncated forms of BAFF-R are referred to hereinafter as“ΔBAFF-R,” or “ΔBAFF-R polypeptides.” Corresponding nucleic acidsencoding ΔBAFF-R polypeptides are referred to as “ΔBAFF-R nucleicacids.”

The present disclosure provides soluble forms of recombinantly expressedΔBAFF-R that possess at least one or more of the following: an alteredglycosylation pattern, an ability to bind to BAFF with an apparentdissociation constant equal to or less than 10⁻⁹ M, and/or a reducedpropensity for aggregation. Among other advantages, these truncatedforms of BAFF-R possess a glycosylation pattern that allows moreefficient analysis of the protein during large-scale production.

In one aspect, the present disclosure provides a truncated form ofBAFF-R, having two O-linked glycosylation sites. In certain embodiments,the truncated BAFF-R is glycosylated at T18 of SEQ ID NO:1. In otherembodiments, the truncated BAFF-R is glycosylated at T41 of SEQ ID NO:1.In yet other embodiments, ΔBAFF-R is glycosylated at both T18 and T41 ofSEQ ID NO:1. Such a glycosylation pattern can be analyzed moreefficiently during large-scale production than the full-length ECD ofBAFF-R.

In certain embodiments, ΔBAFF-R is human (hBAFF-R). In some embodiments,ΔBAFF-R contains point mutations that reduce the propensity of hBAFF-Rto aggregate during recombinant expression, e.g., V21N and L28P of SEQID NO:1. The mutated hBAFF-R is referred to as “vBAFF-R.”

In particular embodiments, ΔBAFF-R comprises amino acids 13 to 43 of SEQID NO:1. In some embodiments, ΔBAFF-R comprises longer amino acidsequences, with the N-terminal amino acid being amino acid 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1and the C-terminal amino acid being 43, 44, 45, 46, 47, 48, or 49 of SEQID NO:1. In illustrative embodiments, ΔBAFF-R comprises amino acids 1 to49 of SEQ ID NO:1.

In additional embodiments, the first amino acid sequence may comprisefull length BAFF-R comprising mutations at S50, S51, T56, or S63 of SEQID NO:1 that remove the ability of the BAFF-R molecule to beglycosylated at these sites. In some embodiments, S50, S51, and T56 ofSEQ ID NO:1 are mutated to remove the glycosylation sites. In otherembodiments, S50, S51, T56, and S63 are mutated to remove theglycosylation sites.

In certain embodiments, ΔBAFF-R is a part of a BAFF-R fusion polypeptidethat comprises (a) a first amino acid sequence encoding ΔBAFF-Rpolypeptide and (b) a second amino acid sequence derived from theconstant region of an immunoglobulin, and optionally, a linker betweenthese sequences.

In certain embodiments of the fusion polypeptide, the first amino acidsequence is substantially identical to amino acids 13 to 43 or aminoacids 14 to 43 of SEQ ID NO:1. In other embodiments, ΔBAFF-R compriseslonger amino acid sequences, with the N-terminal amino acid being aminoacid 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or19 of SEQ ID NO:1 and the C-terminal amino acid being 43, 44, 45, 46,47, 48, or 49 of SEQ ID NO:1. In illustrative embodiments, ΔBAFF-Rcomprises amino acids 1 to 49 of SEQ ID NO:1, amino acids 8 to 49 of SEQID NO:1, amino acids 13 to 49 of SEQ ID NO:1 or amino acids 14 to 49 ofSEQ ID NO:1. In all embodiments, the first amino acid sequence does notinclude amino acids 50 to 56 of SEQ ID NO:1. In some embodiments, thefirst amino acid sequence does not include amino acids 50 to 63 of SEQID NO:1.

The second amino acid sequence may be derived from the constant regionof an immunoglobulin, such as the Fc portion. In certain embodiments,the second amino acid sequence is derived from the Fc portion of an IgG.In related embodiments, the Fc portion is derived from IgG₁, IgG₄ oranother IgG isotype. In particular embodiments, the second amino acidsequence is amino acids 3 to 227 of SEQ ID NO:4 (human IgG₁).

In certain embodiments, the second amino acid sequence is joined to theC-terminus or the N-terminus of the first amino acid sequence by alinker. The exact length and sequence of the linker and its orientationrelative to the linked sequences may vary. The linker may beproteinaceous or non-proteinaceous. In the case of a proteinaceouslinker, it does not include amino acids 50 to 56 of SEQ ID NO:1.

In particular embodiments, ΔBAFF-R-Fc fusion polypeptide (ΔBAFF-R:Fc)comprises at least amino acids 1 to 49, 8 to 49, 14 to 49, 13 to 43, or14 to 43 of SEQ ID NO:1 fused directly to amino acids 3-227 of SEQ IDNO:4. In further embodiments, ΔBAFF-R:Fc comprises amino acids 1 to 49,8 to 49, 14 to 49, 13 to 43, or 14 to 43 of SEQ ID NO:1 joinedindirectly (i.e., through a linker) to amino acids 3 to 227 of SEQ IDNO:4. In some embodiments, ΔBAFF-R:Fc comprises longer BAFF-R sequences,with the N-terminal amino acid being amino acid 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1 and theC-terminal amino acid being amino acid 43, 44, 45, 46, 47, 48, or 49 ofSEQ ID NO:1 fused directly to amino acids 3 to 227 of SEQ ID NO:4 orjoined by a linker.

The disclosure provides ΔBAFF-R nucleic acids encoding ΔBAFF-Rpolypeptides. In some embodiments, the nucleic acid comprises sequencesencoding at least amino acids 13 to 43 of SEQ ID NO:1 or at least aminoacids 14 to 43 of SEQ ID NO:1. The nucleic acid can encode longerfragments of ΔBAFF-R with the N-terminus at amino acid 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1 andthe C-terminus at amino acid 43, 44, 45, 46, 47, 48, or 49 of SEQ IDNO:1. In other embodiments, the nucleic acid comprises nucleotides 1 to216 of SEQ ID NO:2 or nucleotides 1 to 216 of SEQ ID NO:3.

In some embodiments, the invention provides a DNA construct encodingΔBAFF-R joined to a constant region of an immunoglobulin, eitherdirectly or through a linker. In particular embodiments, the DNAconstruct encodes ΔBAFF-R having an N-terminus at amino acid 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1and a C-terminus at amino acid 43, 44, 45, 46, 47, 48, or 49 of SEQ IDNO:1, joined to amino acids 3 to 227 of SEQ ID NO:4. In other particularembodiments, the DNA construct comprises nucleotides 1 to 216 of SEQ IDNO:2 or SEQ ID NO:3 joined to nucleotides 7 to 681 of SEQ ID NO:5.

The disclosure also provides methods and pharmaceutical compositions fortreating B-cell- and T-cell-mediated conditions. The methods includeadministering, to a subject in which such treatment is desired, anucleic acid encoding ΔBAFF-R or a ΔBAFF-R polypeptide in an amountsufficient to treat, prevent, or delay a BAFF-related condition in thesubject. The disorders that can be treated using the compositions andmethods of the present invention include but are not limited todisorders described in WO 02/24909, herein incorporated by reference.These disorders include, but are not limited to, immunologic disorders,autoimmune diseases, cancers, renal diseases, virus-associated diseases,hypertensive diseases, conditions requiring immunosuppression,inflammatory diseases, and non-malignant proliferative disorders.

Additional objects and advantages of the invention will be set forth inpart in the description which follows, and in part will be obvious fromthe description, or may be learned by practice of the invention. Theobjects and advantages of the invention will be realized and attained bymeans of the elements and combinations particularly pointed out in theappended claims.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed.

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments of theinvention and together with the description, serve to explain theprinciples of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows results of co-immunoprecipitation of BAFF with variousΔBAFF-R:Fc. Lane 1 represents amino acids A14 to A72 of SEQ ID NO:1;lane 2 represents amino acids R3 to S50 of SEQ ID NO:1; lane 3represents amino acids R3 to Q59 of SEQ ID NO:1; lane 4 represents aminoacids R3 to G67 of SEQ ID NO:1; lane 5 represents amino acids R3 to A72of SEQ ID NO:1; lane 6 represents molecular weight standards; lane 7represents amino acids R3 to A72 of SEQ ID NO:1; lanes 8 and 9 representamino acids R3 to R43 of SEQ ID NO:1; lane 10 represents amino acids R3to T41 of SEQ ID NO:1; and lane 11 represents amino acids R3 to C36 ofSEQ ID NO:1.

FIG. 2 shows results of a binding assay for determination of k_(D)^(APP) of vBAFF-R(R3-A49):Fc or vBAFF-R(R3-A72):Fc, and BAFF. The openand closed symbols represent the results from duplicate experiments.

FIG. 3 shows an analysis of the estimated k_(D) ^(APP) ofvBAFF-R(R3-A49):Fc or vBAFF-R(R3-A72):Fc, and BAFF. The open and closedsymbols represent the results from duplicate experiments.

FIG. 4 shows the binding of vBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc tohuman BAFF (hBAFF) expressed on the surface of CHO cells.

FIG. 5 shows results of binding assays with various concentrations ofvBAFF-R(R3-A72):Fc or vBAFF-R(R3-A49):Fc to block the binding ofbiotinylated hBAFF to BJAB cells.

FIGS. 6A-6B show the location of predicted N-linked glycosylation siteon murine BAFF-R:Fc (SEQ ID NO:6) and O-linked glycosylation sites onhuman vBAFF-R(R3-A72) (SEQ ID NO:1).

FIG. 7 shows a mass spectrum of vBAFF-R(R3-A72):Fc isolated from a CHOclone, indicating the molecular weights of the O-linked glycosylationforms associated with each peak.

FIGS. 8A-8F show mass spectra of vBAFF-R(R3-A72):Fc's isolated fromvarious CHO clones. FIGS. 8G-8H show, respectively, mass spectra ofvBAFF-R(R3-A72):Fc and mBAFF-R:Fc produced by 293EBNA cells, indicatingmolecular weights of the O-linked glycosylation forms associated witheach peak.

FIG. 9 shows a mass spectrum of vBAFF-R(R3-A49):Fc isolated from a CHOclone, indicating molecular weights of the O-linked glycosylation formsassociated with each peak.

FIG. 10 shows the effect of increasing vBAFF-R(R3-A49):Fc concentrationin the growth media on mouse splenic B cells' ability to incorporate[³H]-thymidine. Triangles represent cultures treated with human IgG asthe inhibitor, squares represent vBAFF-R(R3-A49):Fc treatment, anddiamonds represent vBAFF-R(R3-A72):Fc treatment.

FIG. 11 shows the effect of vBAFF-R(R3-A49):Fc on the number of CD19+splenic B cells.

FIG. 12A shows results of an ELISA capture experiment in which hBAFF wasimmobilized and the binding affinities of vBAFF-R(R3-A49):Fc andvBAFF-R(R3-A72):Fc to BAFF were measured by OD405. FIG. 12B showsresults of a similar ELISA experiment in which vBAFF-R(R3-A49):Fc andvBAFF-R(R3-A72):Fc were immobilized and the binding of FLAG-hBAFF wasmeasured by OD405.

DESCRIPTION OF THE EMBODIMENTS

In order for the present invention to be more readily understood,certain terms are defined herein. Additional definitions are set forththroughout the detailed description.

The term “altered glycosylation pattern” refers to a glycosylationpattern on non-naturally occurring BAFF-R having a C-terminallytruncated extracellular domain as compared to BAFF-R having the fulllength extracellular domain, which may or may not differ from wild typesequence. For human BAFF-R, the C-terminal truncation of theextracellular domain is such that it results in removal of at least oneO-linked glycosylation site.

The term “BAFF” refers to B-cell-activating factor of the TNF family,characterized by expression by monocytes, macrophages, peripheral bloodlymphocytes, and dendritic cells, and its role as a B cell survivalfactor. A summary of BAFF's characteristics is provided in Mackay et al.(2002) Nature Reviews Immunology 2: 465-475.

As used herein, the term “BAFF-R,” unless otherwise stated, refers tomutant or wildtype human BAFF receptor and variants thereof, includingthe splice variant containing an additional alanine at amino acid 50, asset forth in SEQ ID NO:7, a TNF family receptor protein that binds BAFF,but not the other ligands recognized by BCMA and TACI, as defined in WO02/24909. The term “ΔBAFF-R” refers to any form of BAFF-R lacking aminoacids at the N- or C-terminal, but maintaining the ability to bind toBAFF. The term “hBAFF-R” refers to human BAFF-R protein, or a naturallyoccurring variant thereof. The term “vBAFF-R” refers to a mutated formof human BAFF-R having mutations at least at amino acids 21 and 28 ofSEQ ID NO:1, e.g., V21N and L28P.

The term “BAFF-R:Fc” refers to a fusion protein comprising BAFF-R andimmunoglobulin constant region (Fc) sequences. The term “ΔBAFF-R:Fc”refers to any fusion protein comprising (1) at least amino acids 13-43of SEQ ID NO:1 or a variant thereof, however, not including amino acids50-56 of SEQ ID NO:1, and (2) an amino acid sequence derived from theconstant region of an immunoglobulin, e.g., Fc. Similarly, the term“mBAFF-R:Fc” refers to a fusion protein comprising murine BAFF-R and Fcsequences.

The term “correspond” and its cognates, when used in reference to anamino acid residue or its position, refer to an amino acid position in afirst amino acid sequence relative to an amino acid position in a secondamino acid sequence when the first and second sequences are optimallyaligned. Sequences are considered to be optimally aligned when themaximal possible number of amino acids in both sequences match.

The term “biological activity” refers to a function or set of functions(or the effect to which the function is attributed to) performed by amolecule in a biological system, which may be in vivo or in vitro.Biological activity may be assessed by, for example, the effect onlymphocyte proliferation, survival, and function (e.g., cytokinesecretion), cluster of differentiation marker expression, geneexpression at the transcriptional, translational, or post-translationallevels, or the effect on autoantibody production, etc.

The term “extracellular domain (ECD) of BAFF-R” refers to the portion ofthe protein present on the exterior of a cell expressing the protein,specifically amino acids 1 to 72 of SEQ ID NO:1. The term “stalk domain”refers to the portion of a TNF receptor family member protein betweenthe cysteine-rich domain and the transmembrane domain.

The term “immunologic disorder” refers to disorders and conditions inwhich an immune response is aberrant. The aberrant response can be dueto (a) abnormal proliferation, maturation, survival, differentiation, orfunction of immune cells such as, for example, T or B cells. Suchdisorders include but are not limited to rheumatoid arthritis (RA),juvenile chronic arthritis, asthma, psoriasis, demyelinating disorders,multiple sclerosis (MS), inflammatory bowel disease (IBD), inflammatoryand fibrotic lung disease, Crohn's disease, systemic lupus erythematosis(SLE), type I diabetes, transplant rejection, graft-versus-host disease(GVHD), hyperproliferative immune disorders, autoimmune diseases, B cellcancers, immunomodulation, antibody-mediated pathologies (e.g., ITP,myasthenia gravis, and the like), renal diseases, indirect T cell immuneresponse, graft rejection, and graft versus host disease, andimmunosuppressive disorders.

The term “isolated” refers to a molecule that is substantially free ofits natural environment. For instance, an isolated protein issubstantially free of cellular material or other proteins from the cellor tissue source from which it is derived. The term “isolated” alsorefers to preparations where the isolated protein is sufficiently pureto be administered as a pharmaceutical composition, or at least 70-80%(w/w) pure, more preferably, at least 80-90% (w/w) pure, even morepreferably, 90-95% pure; and, most preferably, at least 95%, 96%, 97%,98%, 99%, or 100% (w/w) pure.

The term “modulating” and its cognates refer to a reduction or anincrease in biological activity of BAFF-R or BAFF, e.g., the activityassociated with the effect exerted by naturally expressed BAFF-R or BAFFon a lymphocyte expressing a BAFF receptor. A reduction or an increasein biological activity is preferably at least 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 90%, or more.

The terms “therapeutic compound” and “therapeutic,” as used herein,refer to any compound capable of ameliorating clinical manifestations ofa disorder, or producing a desired biological outcome.

The terms “polynucleotide,” “oligonucleotide,” and “nucleic acid” referto deoxyribonucleic acid (DNA) and, where appropriate, to ribonucleicacid (RNA), or peptide nucleic acid (PNA). The term should also beunderstood to include nucleotide analogs, and single or double strandedpolynucleotides. Examples of polynucleotides include but are not limitedto plasmid DNA or fragments thereof, viral DNA or RNA, antisense RNA,siRNA, etc. The term “plasmid DNA” refers to double stranded DNA that iscircular.

The present invention is based, in part, on the discovery andcharacterization of the glycosylation pattern of human BAFF-R andvariants thereof. In particular, the full-length human BAFF-R comprisesmultiple O-linked glycosylation sites, while the murine version of theprotein contains one N-linked glycosylation site and no O-linkedglycosylation sites. There are five potential glycosylation sites in theC-terminus of human BAFF-R: T41, S50, S51, T56, and S63 of SEQ ID NO:1.A proteolytic fragment containing all five sites was consistently >80%glycosylated (see Table 2).

The present disclosure provides a non-naturally occurring BAFF-Rglycoprotein having a deletion in the ECD that results in alteredO-linked glycosylation pattern. Deletion analysis of the stalk region ofhBAFF-R(R3-A72):Fc indicates that the deletion of residues 44-72 doesnot destroy the ability of the resultant fusion protein to interact withBAFF. The fusion protein vBAFF-R(R3-A49):Fc illustrated in the Examplesis generated by deletion of amino acid residues 50-72 in the stalkregion of vBAFF-R(R3-A72):Fc (described in WO 02/24909).

Determining the exact composition of a protein is an essential step inproducing a pharmaceutically acceptable protein-based therapeutic.Variations in the glycosylation of a polypeptide may lead to changes inimportant characteristics such as binding affinity and solubility. Whenmanufacturing a protein therapeutic, each batch must be analyzed for avariety of important characteristics, including sugar content. Theglycosylation pattern of human BAFF-R can be difficult to analyze andcontrol during product manufacturing. Furthermore, given a potentialbatch-to-batch variability, the analysis of the glycosylation patternmay be necessary for identifying the source of variability. Therefore,among other advantages, the presently disclosed truncated forms ofBAFF-R allow for more efficient analysis during large scale production.

The C-terminal truncation of BAFF-R at amino acid 43 produces apolypeptide with just two O-linked glycosylation sites while retainingthe BAFF-binding ability of full-length BAFF-R. This ΔBAFF-R istypically glycosylated at only two sites (T18 and T41 of SEQ ID NO:1)when expressed in eukaryotic cells. Thus, the invention provides abiologically active ΔBAFF-R with an altered glycosylation pattern ascompared to full-length protein.

The invention is further based, in part, on the discovery that bindingof BAFF-R to BAFF still occurs when the N-terminal and/or the C-terminalregion of the extracellular domain of BAFF-R is deleted. Binding was notreduced after the deletion of amino acids 50-72 of SEQ ID NO:1, and wasonly partially reduced after the deletion of amino acids 43-72 of SEQ IDNO:1.

Optimally, ΔBAFF-R:Fc binds to BAFF with an apparent affinity (k_(D)^(APP)) of less than 1 nM. ΔBAFF-R(R3-49):Fc binds to BAFF-expressingcells as well as the full-length form, and prevents the binding of BAFFto cells expressing endogenous BAFF-R at concentrations similar toBAFF-R:Fc. These findings indicate that truncated and full-lengthBAFF-R:Fc polypeptides possess similar binding affinities for BAFF, andthat these affinities are in the sub-nanomolar range. These results arereported as an apparent affinity, which includes an avidity component.

In one aspect, the present disclosure provides a truncated form ofBAFF-R, having two O-linked glycosylation sites. In certain embodiments,the truncated BAFF-R is glycosylated at T18 of SEQ ID NO:1. In otherembodiments, the truncated BAFF-R is glycosylated at T41 of SEQ ID NO:1.In yet other embodiments, ΔBAFF-R is glycosylated at both T18 and T41 ofSEQ ID NO:1. In additional embodiments, ΔBAFF-R may be glycosylated atS8 of SEQ ID NO:1. Such a glycosylation pattern can be analyzed moreefficiently during large-scale production than that of the full-lengthECD of BAFF-R.

In certain embodiments, ΔBAFF-R is human (hBAFF-R). In some embodiments,ΔBAFF-R contains point mutations that reduce the propensity of hBAFF-Rto aggregate during recombinant expression, e.g., V21N and L28P of SEQID NO:1. The mutated hBAFF-R is referred to as vBAFF-R.

In particular embodiments, ΔBAFF-R comprises amino acids 13 to 43 of SEQID NO:1. In some embodiments, ΔBAFF-R comprises longer amino acidsequences, with the N-terminal amino acid being amino acid 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1and the C-terminal amino acid being 43, 44, 45, 46, 47, 48, or 49 of SEQID NO:1. In illustrative embodiments, ΔBAFF-R comprises amino acids 1 to49 of SEQ ID NO:1.

in certain embodiments, ΔBAFF-R is a part of a BAFF-R fusion polypeptidethat comprises (a) a first amino acid sequence encoding ΔBAFF-Rpolypeptide and (b) a second amino acid sequence derived from theconstant region of an immunoglobulin, and optionally, a linker betweenthese sequences.

In certain embodiments of the fusion polypeptide, the first amino acidsequence is substantially identical to amino acids 13 to 43 of SEQ IDNO:1 or to amino acids 14 to 43 of SEQ ID NO:1. In other embodiments,ΔBAFF-R comprises longer amino acid sequences, with the N-terminal aminoacid being amino acid 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, or 19 of SEQ ID NO:1 and the C-terminal amino acid being 43,44, 45, 46, 47, 48, or 49 of SEQ ID NO:1. In illustrative embodiments,ΔBAFF-R comprises amino acids 1 to 49 of SEQ ID NO:1, amino acids 8 to49 of SEQ ID NO:1, amino acids 13 to 49 of SEQ ID NO:1, or amino acids14 to 49 of SEQ ID NO:1. In all embodiments, the first amino acidsequence does not include amino acids 50 to 56 of SEQ ID NO:1. In someembodiments, the first amino acid sequence does not include amino acids50 to 63 of SEQ ID NO:1.

The second amino acid sequence may be derived from the constant regionof an immunoglobulin, such as the Fc portion. In certain embodiments,the second amino acid sequence is derived from the Fc portion of an IgG.In related embodiments, the Fc portion is derived from IgG₁, IgG₄, oranother IgG isotype. In particular embodiments, the second amino acidsequence is amino acids 3 to 227 of SEQ ID NO:4 (human IgG₁).

In certain embodiments, the second amino acid sequence is joined to theC-terminus or the N-terminus of the first amino acid sequence by alinker. The exact length and sequence of the linker and its orientationrelative to the linked sequences may vary. The linker may beproteinaceous or non-proteinaceous. In the case of a proteinaceouslinker, it does not include amino acids 50 to 56 of SEQ ID NO:1.

In particular embodiments, ΔBAFF-R-Fc fusion polypeptide (ΔBAFF-R:Fc)comprises at least amino acids 1 to 49, 8 to 49, 14 to 49, 13 to 43, or14 to 43 of SEQ ID NO:1 fused directly to amino acids 3-227 of SEQ IDNO:4. In further embodiments, ΔBAFF-R:Fc comprises amino acids 1 to 49,8 to 49, 14 to 49, 13 to 43, or 14 to 43 of SEQ ID NO:1 joinedindirectly (i.e., through a linker) to amino acids 3 to 227 of SEQ IDNO:4. In some embodiments, ΔBAFF-R:Fc comprises longer BAFF-R sequences,with the N-terminal amino acid being amino acid 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1 and theC-terminal amino acid being amino acid 43, 44, 45, 46, 47, 48, or 49 ofSEQ ID NO:1 fused directly to amino acids 3 to 227 of SEQ ID NO:4 orjoined by a linker.

The invention also provides full length BAFF-R molecules comprisingamino acid mutations at S50, S51, T56, or S63 of SEQ ID NO:1 that removethe ability of the BAFF-R molecule to be glycosylated at these sites. Insome embodiments, S50, S51, and T56 of SEQ ID NO:1 are mutated to removethe glycosylation sites. In other embodiments, S50, S51, T56, and S63are mutated to remove the glycosylation sites.

The disclosure provides BAFF-R nucleic acids encoding ΔBAFF-Rpolypeptides. In some embodiments, the nucleic acid comprises sequencesencoding at least amino acids 13 to 43 of SEQ ID NO:1 or at least aminoacids 14 to 43 of SEQ ID NO:1. The nucleic acid can encode longerfragments of ΔBAFF-R with the N-terminus at amino acid 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1 andthe C-terminus at amino acid 43, 44, 45, 46, 47, 48, or 49 of SEQ IDNO:1. In other embodiments, the nucleic acid comprises nucleotides 1 to216 of SEQ ID NO:2 or nucleotides 1 to 216 of SEQ ID NO:3.

In some embodiments, the invention provides a DNA construct encodingΔBAFF-R joined to a constant region of an immunoglobulin, eitherdirectly or through a linker. In particular embodiments, the DNAconstruct encodes ΔBAFF-R having an N-terminus at amino acid 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1and a C-terminus at amino acid 43, 44, 45, 46, 47, 48, or 49 of SEQ IDNO:1, joined to amino acids 3 to 227 of SEQ ID NO:4. In other particularembodiments, the DNA construct comprises nucleotides 1 to 216 of SEQ IDNO:2 or SEQ ID NO:3 joined to nucleotides 7 to 681 of SEQ ID NO:5.

A fusion protein construct can be created by ligating sequences encodingtwo distinct polypeptides in frame such that they are translated in asingle open reading frame. In some embodiments, the invention provides aDNA construct comprising ΔBAFF-R fused to the constant region of anantibody, either directly or with linker DNA that does not includesequence encoding amino acids 50 to 56 of SEQ ID NO:1. In specificembodiments, the nucleic acids can encode a ΔBAFF-R:Fc protein havingthe N-terminus at amino acid 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, or 19 of SEQ ID NO: 1 and the C-terminus at aminoacid 43, 44, 45, 46, 47, 48, or 49 of SEQ ID NO: 1 linked to amino acids3 to 227 of SEQ ID NO:4. In other specific embodiments the nucleic acidscomprise nucleotides 1 to 216 of SEQ ID NO:2 linked to nucleotides 7 to681 of SEQ ID NO:5.

ΔBAFF-R and its encoding nucleic acid molecules and vectors may beproduced using any suitable cloning methods. Systems for cloning andexpression of a polypeptide in a variety of different host cells arewell known. Suitable host cells include bacteria, mammalian cells, andyeast and baculovirus systems. Mammalian cell lines available in the artfor expression of a heterologous polypeptide include Chinese hamsterovary cells, HeLa cells, baby hamster kidney cells, NS0 mouse melanomacells and many others. A common bacterial host is E. coli. Bacterialcells, such as E. coli, do not add N-linked or O-linked glycosylation tothe polypeptide. Yeast and baculovirus do make N-linked or O-linkedglycosylation modifications, but the sugar residues may be of differentcomposition in these cells than those utilized by mammalian cells. Forother cells suitable for producing ΔBAFF-R, see Gene Expression Systems,eds. Fernandez et al. (1999) Academic Press.

Suitable vectors can be chosen or constructed, containing appropriateregulatory sequences, including promoter sequences, terminatorsequences, polyadenylation sequences, enhancer sequences, marker genesand other sequences as appropriate. Vectors may be plasmid or viral,e.g., phage, or phagemid, as appropriate. For further details see, e.g.,Molecular Cloning: A Laboratory Manual, Sambrook et al. (1989) 2nd ed.,Cold Spring Harbor Laboratory Press. Many known techniques and protocolsfor manipulation of nucleic acid, for example, in preparation of nucleicacid constructs, mutagenesis, sequencing, introduction of DNA into cellsand gene expression, and analysis of proteins, are described in detailin Current Protocols in Molecular Biology, eds. Ausubel et al. (1992)2nd ed., John Wiley & Sons.

The ΔBAFF-R polypeptides of the invention and nucleic acids encodingthem can be incorporated into pharmaceutical compositions suitable foradministration. Such compositions typically comprise the nucleic acid orpolypeptide and a pharmaceutically acceptable carrier. As used herein,“pharmaceutically acceptable carrier” is intended to include anysolvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents, and others that arecompatible with pharmaceutical administration. Suitable carriers aredescribed in detail in WO 02/24909.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. A therapeuticallyeffective amount of ΔBAFF-R ranges from 0.001 to 30 mg/kg, preferablyfrom 0.01 to 25 mg/kg, from 0.1 to 20 mg/kg, or from 1 to 10 mg/kg bodyweight. The dosage may be adjusted, as necessary, to suit observedeffects of the treatment. ΔBAFF-R may given as a bolus dose. Continuousinfusion may also be used after the bolus dose. The appropriate dose andregimen is chosen based on clinical indications by a treating physician.Examples of routes of administration and appropriate compositions foreach of these routes are described in detail in WO 02/24909. Additionalmethods and therapeutic regiments are described in detain in U.S.Application Ser. No. 60/512,880.

The nucleic acids of the invention can be inserted in vectors and usedas gene therapy vectors or delivered as naked DNA. Examples of genetherapy vectors and delivery thereof can be found in WO 02/24909.

The present invention provides both prophylactic and therapeutic methodsof treating a subject at risk of (or susceptible to) a BAFF-relateddisorder (a disorder associated with aberrant BAFF or BAFF-R expressionor activity such as, for example, in B-cell- and T-cell-mediatedconditions). Diseases and disorders that are characterized by increasedlevels or biological activity of BAFF may be treated with therapeuticsthat antagonize BAFF or BAFF-R activity. The methods includeadministering, to a subject in which such treatment is desired, anucleic acid encoding ΔBAFF-R or a ΔBAFF-R polypeptide in an amountsufficient to treat, prevent, or delay a BAFF-related condition in thesubject. The disorders that can be treated using the compositions andmethods of the present invention include but are not limited todisorders described in WO 02/24909.

Administering the ΔBAFF-R composition can occur prior to themanifestation of symptoms characteristic of the BAFF-R activity, suchthat a disease or disorder is prevented or, alternatively, delayed inits progression.

Another aspect of the invention pertains to methods of modulating BAFFor BAFF-R expression or activity for therapeutic purposes. Themodulatory methods of the invention involves contacting a cell with aΔBAFF-R polypeptide or nucleic acid that modulates one or more of theactivities of BAFF activity associated with the cell. In one embodiment,the ΔBAFF-R composition inhibits one or more BAFF activities. Themodulation can be performed in vitro (e.g., by culturing a cell with thecomposition) or, alternatively, in vivo (e.g., by administering theagent to a subject). As such, the present invention provides methods oftreating an individual afflicted with a disease or disorder involvingBAFF activity by administering a ΔBAFF-R protein or nucleic acid toblock BAFF activity.

The disclosure provides methods and pharmaceutical compositions fortreating autoimmune diseases, B cell cancers, immunomodulation,inflammatory bowel disease, and any antibody-mediated pathologies (e.g.,ITP, myasthenia gravis, and the like), renal diseases, indirect T cellimmune response, graft rejection, and graft versus host disease. Thecompositions of the invention can be targeted to specifically regulate Bcell responses during the immune response. Additionally, thecompositions of the invention can be used to modulate B celldevelopment, development of other cells, antibody production, andcytokine production. Compositions of the invention can also modulate Tand B cell communication by neutralizing the proliferative effects ofBAFF.

The ΔBAFF-R nucleic acids and polypeptides can also be useful for thetreatment of autoimmune disorders including, but not limited to, lupusand rheumatoid arthritis. By modulating BAFF activity, ΔBAFF-R mayprevent or reduce the symptoms of these diseases. The ΔBAFF-R-mediatedmodulation of the symptoms of these diseases may occur by the reductionof B cell development, development of other cells, antibody production,or cytokine production. The effect of ΔBAFF-R on lupus may be measuredby evaluating autoantibody levels, immune complex depositioncomplications, and symptoms of systemic lupus erythematosis, includingkidney failure, proteinuria, splenomegaly, neuralgic symptoms, anddeath. The effect of ΔBAFF-R on rheumatoid arthritis may be measured byevaluating autoantibody levels, the secretion of arthritogenicimmunoglobulins, joint and extremity swelling, or cytokine levels. Inaddition, ΔBAFF-R may be useful for treating other autoimmune disorderssuch as myasthenia gravis and juvenile chronic arthritis.

ΔBAFF-R nucleic acids and polypeptides can be useful for neutralizingthe effects of BAFF for treating pre-B or B-cell leukemias, such asplasma cell leukemia, chronic or acute lymphocytic leukemia, myelomas(e.g., multiple myeloma, plasma cell myeloma, endothelial myeloma, andgiant cell myeloma), and lymphoma (e.g., non-Hodgkin's lymphoma).Additional examples of B cell lymphomas that may be treated with themolecules described herein include Burkitt's lymphoma, non-Burkitt'slymphoma, follicular lymphoma, acute lymphoblastic leukemia, large celllymphoma (e.g., immunoblastic lymphoma), marginal zone lymphoma, mantlecell lymphoma, small lymphocytic lymphoma, and other B cell lymphomas.

The invention provides methods employing ΔBAFF-R polypeptides andnucleic acids for selectively blocking or neutralizing the actions of Bcells in association with end stage renal diseases, which may or may notbe associated with autoimmune diseases. Such methods would be useful fortreating immunologic renal diseases, e.g., glomerulonephritis associatedwith diseases such as membranous nephropathy, IgA nephropathy, orBerger's disease, IgM nephropathy, Goodpasture's disease,post-infectious glomerulonephritis, mesangioproliferative disease,chronic lymphoid leukemia, and minimal-change nephritic syndrome. Suchmethods would also serve as therapeutic applications for treatingsecondary glomerulonephritis or vasculitis associated with such diseasesas lupus, polyarteritis, Henoch-Schonlein disease, Scleroderma,HIV-related diseases, amyloidosis, or hemolytic uremic syndrome. Themethods of the present invention would also be useful as part of atherapeutic application for treating interstitial nephritis orpyelonephritis associated with chronic pyelonephritis, analgesic abuse,nephrocalcinosis, nephropathy caused by other agents, nephrolithiasis,or chronic or acute interstitial nephritis. The methods of the presentinvention also include the use of ΔBAFF-R nucleic acids or polypeptidesin the treatment of hypertensive or large vessel diseases, includingrenal artery stenosis or occlusion and cholesterol emboli or renalemboli, renal or urological neoplasms, multiple myelomas, lymphomas,light chain neuropathy, or amyloidosis with compositions comprisingΔBAFF-R.

The invention also provides methods for blocking or inhibiting activatedB cells using ΔBAFF-R polypeptides for the treatment of asthma and otherchronic airway diseases such as bronchitis and emphysema.

Also provided are methods for inhibiting or neutralizing an effector Tcell response using ΔBAFF-R polypeptides. These methods can be used totreat conditions requiring immunosuppression, such as graft-versus-hostdisease and graft rejection. ΔBAFF-R compositions are also useful fortreatment of autoimmune diseases like insulin dependent diabetesmellitus and Crohn's disease. Methods of the present invention wouldhave additional therapeutic value for treating chronic inflammatorydiseases, in particular, to lessen joint pain (e.g, in trauma orosteoarthritis), swelling, anemia, and other associated symptoms as wellas for treating septic shock.

Additionally, the present invention is useful for the treatment ofproliferative conditions that are not considered to be tumors, i.e.,cellular hyperproliferation (hyperplasia), such as, for example,scleroderma, pannus formation in rheumatoid arthritis, postsurgicalscarring and lung, liver and uterine fibrosis.

Example 1

This example describes the generation and analysis of various peptidedeletions within the receptor domain of wild type hBAFF-R:Fc. Thesedeletion mutants were analyzed for ability to bind hBAFF.

Double stranded oligonucleotide cassettes with cohesive ends that encodevarious in-frame peptide deletions within the hBAFF-R domain ofhBAFF-R:Fc were designed and synthesized. The oligonucleotide cassetteswere ligated with hBAFF-R:Fc containing vectors with complementarytermini. Cassettes were designed to eliminate residues either N-terminalto the cysteine-rich domain (CRD) or C-terminal to the CRD in the stalkregion.

The coding sequences for hBAFF-R:Fc deletions were subcloned intovectors for mammalian cell expression in 293EBNA cells. Expressionplasmids were transfected into 293EBNA cells using Lipofectamine™(Invitrogen). Transfected cell supernatants were harvested at 48 hrpost-transfection.

Expression was evaluated by non-reducing SDS-PAGE followed by Westerntransfer to PVDF membranes. Membranes were blocked for one hour with 5%non-fat dry milk in TBST (10 mM Tris-Cl, 150 mM NaCl, 0.05% Tween 20™),probed with an HRP-conjugated anti-human IgG antibody (JacksonImmunoResearch), washed three times in TBST, and detected with achemiluminescent substrate (ECL, Amersham-Pharmacia).

The ability to bind hBAFF was analyzed by co-immunoprecipitation. Inthese experiments, 100 μl of conditioned media containing hBAFF-R:Fc ora deletion thereof were incubated 3 hrs or overnight at 4° C. in 1 mlDMEM-10% FBS with 100 ng/ml soluble flag-hBAFF. Protein A Sepharose™beads, 30 μl, were added and incubated continued with agitation for anadditional 90 minutes. Beads were centrifuged briefly and washed 3 timeswith 1 ml cold PBS. Beads were resuspended in reducing Laemmli buffer,boiled, and run on SDS-PAGE. Western blots were performed as describedabove with 5 μg/ml anti-flag-HRP (Sigma Chemical) used as a probe.

The coding sequences for the various deletions of hBAFF-R:Fc werescreened by various restriction digests and verified by DNA sequencing.All of the constructs expressed Fc fusion proteins at moderate levelsbut aggregation was not alleviated as compared to hBAFF-R(R3-A72):Fc.Co-immunoprecipitation results are shown in FIG. 1 and summarized inTable 1. In FIG. 1, lane 1 represents amino acids A14 to A72 of SEQ IDNO:1; lane 2 represents amino acids R3 to S50 of SEQ ID NO:1; lane 3represents amino acids R3 to Q59 of SEQ ID NO:1; lane 4 represents aminoacids R3 to G67 of SEQ ID NO:1; lane 5 represents amino acids R3 to A72of SEQ ID NO:1; lane 6 represents molecular weight standards; lane 7represents amino acids R3 to A72 of SEQ ID NO:1; lanes 8 and 9 representamino acids R3 to R43 of SEQ ID NO:1; lane 10 represents amino acids R3to T41 of SEQ ID NO:1; and lane 11 represents amino acids R3 to C36 ofSEQ ID NO:1. The N-terminal deletion hBAFF-R(A14-A72):Fc retains BAFFbinding ability while hBAFF-R(C20-A72):Fc does not. This indicates thatall or a subset of the five amino acid residues immediately N-terminalto the hBAFF-R CRD are required for BAFF binding of hBAFF-R:Fc. BAFFbinding was eliminated in C-terminal deletions hBAFF-R(R3-C36):Fc andhBAFFR(R3-T41):Fc, and profoundly reduced in hBAFF-R(R3-R43):Fc. Allother hBAFF-R:Fc constructs tested that encode BAFF-R through S50 orgreater in the hBAFF-R stalk domain are able to co-immunoprecipitatehBAFF as effectively as the full stalk version, hBAFF-R(R3-A72):Fc.Since truncation at R43 allows for partial binding activity andtruncation at S50 allows for full activity, it is apparent that residuesP44-A49 or a subset thereof are required for proper ligand binding tooccur.

TABLE 1 N-terminus C-termimus BAFF of BAFF-R of BAFF-R binding moietymoiety Comments (co-IP) R3 A72 full length R-Fc +++ R3 G67 eliminatesshort hydrophobic +++ stretch in c-terminal domain R3 Q59 best alignmentwith hBCMA-Fc +++ hydrophobicity plot R3 S50 intermediate lengthC-terminal +++ deletion R3 R43 intermediate length C-terminal + deletionR3 T41 intermediate length C-terminal − deletion R3 C36 maximalC-terminal deletion − without interrupting cysteine-rich domain A14 A72eliminates highly basic stretch in +++ N-terminal domain C20 A72 maximalN-terminal deletion − without interrupting cysteine-rich domain R3 G82addition of 10 residues of potential +++ stalk domain

Example 2

This example describes the design, construction and sequence of aversion of vBAFF-R(R3-A72):Fc containing a truncated BAFF-R stalkdomain. The fusion protein vBAFF-R(R3-A49):Fc was created in order toremove the four potential O-linked glycosylation sites located atresidues S50, S51, T56, and S63 of SEQ ID NO:1.

A double stranded oligonucleotide cassette with cohesive ends was usedto replace nucleotides encoding BAFF-R amino acid residues C33 to A72with nucleotides encoding amino acid residues C33 to A49 by ligationinto the same sites in the vBAFF-R(R3-A72):Fc coding sequence. Thesequences of these oligonucleotides, baf-911 and baf-912, are shown inSEQ ID NO:8 and SEQ ID NO:9. This oligonucleotide replacement results inthe elimination of residues S50-A72 of vBAFF-R(R3-A72):Fc.

The vBAFF-R(R3-A49):Fc coding sequence was subcloned into vectors formammalian cell expression, specifically, 293EBNA or CHO cells.Expression plasmids were transfected into 293EBNA cells usingLipofectamine® (Invitrogen). Transfected cell supernatants wereharvested at 96 hours post transfection. The fusion proteinvBAFF-R(R3-A49):Fc was purified by protein A affinity chromatography andgel filtration size exclusion chromatography.

Example 3

This example illustrates the determination of the apparent bindingaffinity of both full-length vBAFF-R:Fc and truncated vBAFF-R:Fc forBAFF by analysis of their solution phase binding by BIAcore™.

All measurements were made on a BIAcore™ 3000. BCMA-Fc was immobilizedto a high density on one quadrant of a CM5 chip, and one quadrant wasleft underivatized as a background control.

A standard curve for the amount of free BAFF was established by runningsuccessive samples containing various concentrations of BAFF over thechip surfaces. The initial rate of binding (V_(i)) was plotted as afunction of BAFF concentration. Under the conditions used V_(i) isproportional to the amount of free BAFF in solution.

As shown in FIG. 2, the equilibrium binding of BAFF to each form ofBAFF-R:Fc, in solution, was determined by pre-mixing variousconcentrations of BAFF with a fixed amount of either vBAFF-R(R3-A72):Fcor vBAFF-R(R3-A49):Fc, and allowing these solutions to come toequilibrium. These solutions were then run over the BCMA-Fc chip surfaceand the amount of free BAFF in each solution was determined from V_(i)by comparison to the standard curve. The affinity and stoichiometry ofbinding were determined by fitting the data to the appropriate quadraticequation.

As shown in FIG. 3, the equilibrium binding of BAFF tovBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc in solution was determined bypre-mixing various concentrations of each form of variant BAFF-R:Fc witha fixed amount of SAFE and allowing these solutions to come toequilibrium. These VBAFF-R:Fc/BAFF mixtures were then run over theBCMA-Fc chip surface and the amount of free BAFF in each solution wasdetermined from V_(i). The affinity and stoichiometry of binding weredetermined by fitting the data to the appropriate quadratic equation.

As displayed in FIGS. 2 and 3, the binding affinities ofvBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc for BAFF are identical bythese methods. vBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc bind to BAFF insolution with an apparent K_(D)<200 pM and a 1:1 (BAFF:BAFF-R:Fc)stoichiometry.

Example 4

This example illustrates the ability of vBAFF-R(R3-A49):Fc to bind to aCHO cell line stably expressing human BAFF on its surface (CHO:hBAFF).

Three-fold serial dilutions, ranging from 9 μg/ml to 4 ng/ml, ofpurified vBAFF-R(R3-A72):Fc or vBAFF-R(R3-A49):Fc were incubated for onehour on ice with CHO:hBAFF cells (5×10⁶ cells/ml). Cells were washedwith FACS buffer and stained with donkey anti-human IgG-PE (JacksonImmunoReseach) for 30 minutes on ice. Cells were washed in FACS bufferand fixed in 1% paraformaldehyde. Cells were analyzed by FACS for PEfluorescence and the mean fluorescence of the histograms was plotted.

FIG. 4 shows the binding curves for vBAFF-R(R3-A72):Fc andvBAFF-R(R3-A49):Fc to CHO:hBAFF cells. The two curves nearly overlay oneanother and show similar values for half-maximum binding to theCHO:hBAFF cells.

Example 5

This example illustrates the ability for vBAFF-R(R3-A72):Fc andvBAFF-R(R3-A49):Fc to block the binding of hBAFF to BJAB cells, a humanB cell line that expresses hBAFF-R on its surface.

Biotinylated myc-hBAFF was simultaneously added to BJAB cells (5×10⁶cells/ml) with either FACS™ buffer or with three-fold serial dilutionsof purified vBAFF-R(R3-A72):Fc or vBAFF-R(R3-A49):Fc. The finalconcentration of biotinylated hBAFF was 200 ng/ml and the concentrationsof the vBAFF-R:Fc molecules ranged from 9 μg/ml to 4 ng/ml. The cellswere incubated with these solutions on ice for one hour. Cells werewashed with FACS™ buffer, stained with SAV-PE on ice for 30 min, washedagain and fixed in 1% paraformaldehyde. The cells were analyzed by FACS™for PE fluorescence and the mean fluorescence of the histograms wasplotted.

FIG. 5 shows the curves for the ability of various concentrations ofvBAFF-R(R3-A72):Fc or vBAFF-R(R3-A49):Fc to block the binding ofbiotinylated hBAFF to BJAB cells. The two curves nearly preciselyoverlay one another. Half-maximal inhibition of hBAFF binding to BJABcells for vBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc are similar.

Example 6

This example demonstrates the glycosylation patterns of humanvBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc. The predicted N-linkedglycosylation site in the mouse BAFF-R molecule and O-linkedglycosylation sites in the human BAFF-R molecule are shown in FIGS. 6Aand 6B.

vBAFF-R(R3-A72):Fc and vBAFF-R(R3-A49):Fc were expressed and purifiedfrom CHO cells by incubation with Protein A Sepharose™, acid elution,and gel filtration chromatography. After treatment with PNGase F toremove N-linked glycans, the proteins were reduced with DTT, andmolecular mass was determined using a ZMD mass spectrometer. Themolecular masses were generated by deconvolution with the MasEnt 1program.

The detectable peaks in the mass spectrum in FIG. 7 show that there arenumerous O-linked forms of the vBAFF-R(R3-A72):Fc protein. For eachdetectable peak, there are numerous different potential glycosylationpatterns amongst the six potential O-linked glycosylation sites presentin the molecule. The percent occupancy of some of these sites is shownin Table 2. FIGS. 8A-8H show the mass spectra for the vBAFF-R(R3-A72):Fcprotein expressed in different CHO cell lines (FIGS. 8A-F) and a 293cell line (FIG. 8G). FIG. 8H shows a mass spectrum for mBAFF-R:hFc.

Table 2 represents a summary of a series of experiments analyzing theglycosylation of specific potential glycosylation sites invBAFF-R(R3-A72):Fc protein. The proximity of T41, S50, S51, T56, and S63prevents the determination of which site is occupied. However, aproteolytic fragment containing these five sites has an 80% chance ofbeing glycosylated, while a fragment containing just the T18 site is hasonly a 20-40% chance of being glycosylated. This unpredictability in theglycosylation pattern and the inability to determine the source of anygiven glycans creates problems for large-scale production of theprotein.

TABLE 2 Recovery O-linked Carbohydrates Post- Occupancy CHO Post- bufferProductivity Occupancy at T41/S50/ Hydroxylated clone PA exchange (mg/L)at T18 S51/T56/S63 Pro-52  2-11 4.2 3 30 29% 83% 37% 2-6 1.9 1 10 20%83% 30% 2-1 3.2 1.5 15 26% 80% 32% 22 2.7 2.1 21 40% 93% 39% 18 3.4 2.626 35% 94% 31%  7 3 1.6 16 31% 91% 32% 52 2.2 1.7 17 28% 87% 30% 60 1.71.6 16 26% 83% 30% 3-1 2 1.8 18 28% 88% 27% mBAFFR 18.2 18 15.1 N/A N/AN/A hFc 7068-44  vBAFFR N/A N/A N/A 30-40% 80-90% N/A Fc 293 

The mass spectrum of vBAFF-R(R3-A49) is shown in FIG. 9 and summarizedin Table 3.

TABLE 3 Calculated mass Detected (N-deglycosylated mass Probableassignment and reduced) 29914 Residues 8-276 (major component) 2991430572 Residues 8-276 + (HexNAc)(Hex) 30279 30572 Residues 8-276 + 30571(HexNAc)(Hex)(NeuAc) 30862 Residues 8-276 + 30862 (HexNAc)(Hex)(NeuAc)₂31230 Residues 8-276 + 31227 (HexNAc)₂(Hex)₂(NeuAc)₂ 31520 Residues8-276 + 31519 (HexNAc)₂(Hex)₂(NeuAc)₃ 31810 Residues 8-276 + 31810(HexNAc)₂(Hex)₂(NeuAc)₄

The glycosylation pattern of vBAFF-R(R3-A49):Fc polypeptide is muchsimpler than full-length ECD BAFF-R, vBAFF-R(R3-A72):Fc. This shorterpolypeptide contains only two potential O-linked glycosylation sites(T18 and T41). There are only seven peaks in this spectrum, each ofwhich represents a small number of possible glycosylation patterns. Forexample, the 30572 peak represents a ΔBAFF-R:Fc protein with one coredisaccharide (HexNAc)(Hex) linked to either T18 or T41. The mostglycosylated species is the 31810 peak, in which each of the two coredisaccharides are derivatized with two sialic acids(NeuAc). Whencompared to the full-length extracellular domain of BAFF-R, this alteredglycosylation pattern allows for easier characterization of thevariability between batches of pharmaceutical compositions comprisingBAFF-R. Table 4 represents a summary of the analysis of glycosylationsite occupancy and O-linked sugar profile of the two potentialglycosylation sites in vBAFF-R(R3-A49):Fc (Thr-18 and Thr-41).

TABLE 4 O-linked sugar profile HexNAc- HexNAc- Total HexNAc- Hex- Hex-Site occupancy HexNAc Hex NeuAc (NeuAc)₂ Thr-18 40% 10% 5% 5% 20% Thr-4170% 0% 10% 20% 40%

Example 7

This example illustrates the ability of vBAFF-R(R3-A72) andvBAFF-R(R3-A49):Fc to inhibit the B cell survival activity of hBAFF onmouse splenic B cells. BAFF induced cell proliferation assay wasperformed using mouse splenic B cells. Mouse B cells were isolated fromthe spleens of two one month old C57/black6 mice using a B cell recoverycolumn (Cedarlane Labs). B cells were incubated in flat-bottom 96-wellplates (10⁵ cells/well in 100 μl RPMI supplemented with 10% FBS) for 72hours in the presence of 5 μg/ml of goat anti-mouse p chain antibody(Jackson ImmunoResearch), 75 ng/ml of myc-hBAFF, and serial dilutions ofvBAFF-R(R3-A49):Fc, vBAFF-R(R3-A72), or human IgG. Cells were pulsed foran additional 18 hours with [³H]-thymidine (1 μCi/well) and harvested.[³H]-thymidine incorporation was monitored by liquid scintillationcounting. FIG. 10 shows that, in vitro, vBAFF-R(R3-A49):Fc, andvBAFF-R(R3-A72) inhibit BAFF-mediated B cell proliferation equally well,as demonstrated by reduced [³H]-thymidine incorporation when compared tocells incubated with hIgG.

Example 8

This example shows that in vivo BAFF blockade with vBAFF-R(R3-49):Fcimpairs B cell survival, resulting in a reduction in the number ofperipheral B cells, and causes a reduction in the level of expression ofthe B cell surface markers, CD21 and CD23.

A total of 37 female BALB/c mice were assigned to 8 treatment groups asshown in Table 5. All animals were dosed with 200 μl ofvBAFF-R(R3-49):Fc or hIgG intraperoneally (10 ml/kg dose volume). 96hours post-dose mice were euthanized and spleens were harvested forquantitation of B cells.

TABLE 5 Number of animals in Dose level Group Test article group (mg/kg)5 Truncated 3 0.05 6 vBAFF-R:Fc 3 0.25 7 4 0.5 8 3 5 9 Human IgG 3 0.0510 (hIgG) 3 0.25 11 2 0.5 12 3 5

Splenocytes were prepared by mechanical disruption. Debris waseliminated by passing through a 100 μm cell strainer. Red cells werelysed in 5 ml of ACK solution (155 mM ammonium chloride, 10 mM potassiumbicarbonate, 0.1 mM EDTA, pH 7.3), then washed 3 times in 10 ml PBS andsuspended in FACS buffer (0.5% FBS, 0.01 sodium azide). Debris waseliminated by passing through a 100 μm cell strainer, and viable cellswere counted using trypan blue exclusion.

FACS staining: 2 million cells were stained/sample in a volume of 100μl. Cells were incubated on ice with Block buffer (FACS™ buffer with 10μg/ml Fc Block, 5% rat serum) to prevent FcgR (Fc gamma receptor) onsplenocytes from interacting with the Fc domain of the mAbs, therebyminimizing background staining. Specific cocktails of mAbs were addedand incubated on ice for 30 minutes. Cells were washed with FACS™buffer, then suspended in FACS™ buffer containing streptavidin-PerCP(Streptavidin-Peridinin chlorophyll-a Protein, a fluorescent taggedstreptavidin used to detect the biotin-CD23 probe) and incubated on icefor 30 minutes. Cells were washed in FACS buffer and suspended in 150 μl0.5% paraformaldehyde in PBS for analysis in a FACSCaliber™flowcytometer. 100,000 events were collected, and analysis was doneusing CellQuest™ software. Statistical analysis was performed usingStudent's t test.

The numbers of splenic B cells were calculated based on total splenocytenumber and percent of CD19+ cells. As seen in FIG. 11,vBAFF-R(R3-49):Fc-treated mice exhibited a marked loss of splenic Bcells when compared to controls. B cell loss was observed with a dose aslow as 0.25 mg/kg, and the percent loss increased with higher doses ofvBAFF-R(R3-49):Fc.

The impact of BAFF inhibition with vBAFF-R(R3-49):Fc on splenic mature(IgM^(lo)IgD^(hi)) and marginal zone (MZ) (IgM^(hi)IgD^(lo)) B cell CD21and CD23 expression was examined. CD21 mean fluorescence intensity (MFI)was significantly diminished on all B cell subsets examined in the 0.25,0.5, and 5 mg/kg dose groups that received vBAFF-R(R3-49):Fc, whencompared to hIgG-treated controls (Table 6).

TABLE 6 Dose (mg/kg) Treatment Mature B^(a) MZ B^(a) 5 hIgG 28.5 ±3.4^(b) 97.4 ± 10.2 vBAFF-R:Fc 12.5 ± 0.9* 69.3 ± 10* 0.5 hIgG 28.7 ±0.6   84 ± 0.6 vBAFF-R:Fc 17.6 ± 0.9*   66 ± 3.7* 0.25 hIgG 25.5 ± 0.391.2 ± 3.1 vBAFF-R:Fc   20 ± 1.4*   76 ± 5.1 0.05 IgG 31.8 ± 1.5 90.1 ±1.8 vBAFF-R:Fc 31.9 ± 0.7 87.4 ± 3.9 ^(a)Cells obtained from spleens forFACS ™ analysis ^(b)Mean fluorescence intensity ± standard deviation *p< 0.05

CD23 expression was significantly reduced on mature and MZ B cells fromvBAFF-R(R3-49):Fc-treated mice when compared hIgG-treated controls atthe 5 mg/kg dose (Table 7).

TABLE 7 Dose (mg/kg) Treatment Mature B^(a) MZ B^(a) 5 hIgG 105.1 ±18^(b) 29.2 ± 0.6 vBAFF-R:Fc  64.3 ± 4.5*  18.2 ± 2.1* 0.5 hIgG 211.1 ±3.8 51.7 ± 5   vBAFF-R:Fc   201 ± 12.9 41.1 ± 0.9 0.25 hIgG   199 ± 7.160.2. ± 3.1  vBAFF-R:Fc 195.9 ± 11.4 52.3 ± 5.3 0.05 hIgG 175.5 ± 8.8  77 ± 9.6 vBAFF-R:Fc 173.2 ± 9.9 62.6 ± 5.7 ^(a)Cells obtained fromspleens for FACS ™ analysis ^(b)Mean fluorescence intensity ± standarddeviation *p < 0.05

Example 9

This examples illustrates the binding between flag-huBAFF andvBAFF-R(R3-A49):Fc or vBAFF-R(R3-A72):Fc in two ELISA formats. ELISAplates were coated with a capture antibody at 50 μl/well at 5 μg/ml in50 mM sodium bicarbonate pH 9.6 overnight at 4° C. Capture antibodieswere anti-human IgG Fc (Jackson ImmunoResearch) or M2 anti-FLAG (Sigma).Plates were blocked with 3% BSA in PBS at room temperature (RT) for 30minutes and washed 3 times with 250 μl of PBS+0.05% Tween 20™. Allsubsequent incubations were at RT with reagents diluted in 3% BSA-PBS.

On the anti-human IgG Fc coated plate, 50 μl of vBAFF-R(R3-A49):Fc orvBAFF-R(R3-A72):Fc were captured at 2 μg/ml for 2 hours and then washedas above (FIG. 12A). Ten-fold serial dilutions starting at 10 μg/ml of50 μl of FLAG-huBAFF were added, incubated for 30 minutes and washed. M2anti-FLAG at 1 μg/ml, 100 μl, was added for 30 minutes and washed. A1:3000 dilution of anti-murine IgG alkaline phosphatase conjugate(Jackson ImmunoResearch), 100 μl, for 30 minutes.

On the anti-FLAG coated plate, 50 μl of 10 μg/ml FLAG-huBAFF was addedand incubated for 2 hours and washed as above (FIG. 12B). Ten-foldserial dilutions starting at 10 μg/ml of 50 μl of vBAFF-R(R3-A49):Fc andvBAFF-R(R3-A72):Fc were added and incubated for 30 minutes and washed asabove. A 1:3000 dilution of anti-human Fc gamma alkaline phosphataseconjugate (Jackson ImmunoResearch) (1:3000 dilution), 100 μl, for 30minutes.

After washing, detection for both sets of plates was achieved byincubation with 100 μl of 2 mg/ml pNpp (Pierce) in 10% diethanolaminepH9.0, 1 mM MgCl₂, 1 mM ZnCl₂ at room temperature until sufficient colorformation was observed. OD₄₀₅ was read.

As shown in FIGS. 12A and 12B, under both ELISA formats, the IC50 forligand binding for vBAFF-R(R3-A49):Fc and vBAFF-R(R3-A72):Fc show thesame high functional affinity for FLAG-huBAFF, regardless if ligand orreceptor Fc fusion is in solution.

The specification is most thoroughly understood in light of theteachings of the references cited within the specification, which arehereby incorporated by reference. The embodiments within thespecification provide an illustration of embodiments of the inventionand should not be construed to limit the scope of the invention. Theskilled artisan readily recognizes that many other embodiments areencompassed by the invention. All publications and patents cited andsequences identified by accession or database reference numbers in thisdisclosure are incorporated by reference in their entirety. To theextent the material incorporated by reference contradicts or isinconsistent with the present specification, the present specificationwill supersede any such material. The citation of any references hereinis as not an admission that such references are prior art to the presentinvention.

Unless otherwise indicated, all numbers expressing quantities ofingredients, cell culture, treatment conditions, and so forth used inthe specification, including claims, are to be understood as beingmodified in all instances by the term “about.” Accordingly, unlessotherwise indicated to the contrary, the numerical parameters areapproximations and may very depending upon the desired properties soughtto be obtained by the present invention. Unless otherwise indicated, theterm “at least” preceding a series of elements is to be understood torefer to every element in the series. Those skilled in the art willrecognize, or be able to ascertain using no more than routineexperimentation, many equivalents to the specific embodiments of theinvention described herein. Such equivalents are intended to beencompassed by the following claims.

1. A non-naturally occurring BAFF-R glycoprotein having a deletion inthe extracellular domain which results in altered O-linked glycosylationpattern, wherein the BAFF-R glycoprotein retains the ability to bind toBAFF.
 2. The BAFF-R glycoprotein of claim 1, having at least oneO-linked glycan.
 3. The BAFF-R glycoprotein of claim 1, wherein theO-linked glycan is attached on an amino acid that corresponds tothreonine 18 or threonine 41 of SEQ ID NO:1.
 4. The BAFF-R glycoproteinof claim 1, wherein the O-linked glycan is attached on an amino acidwhich corresponds to threonine 18, threonine 41, or serine 8 of SEQ IDNO:1.
 5. The BAFF-R glycoprotein of claim 1, wherein BAFF-R glycoproteinis human.
 6. The BAFF-R glycoprotein of claim 5, wherein the deletion isselected from the group consisting of: a) from amino acid 50 to aminoacid 56 of SEQ ID NO:1; b) from amino acid 50 to amino acid 63 of SEQ IDNO:1; and c) from amino acid 50 to amino acid 72 of SEQ ID NO:1. 7-10.(canceled)
 11. The BAFF-R glycoprotein of claim 5, having at least twoamino acid substitutions, wherein the substituted amino acid correspondsto amino acid positions 21 and 28 of SEQ ID NO:1.
 12. The BAFF-Rglycoprotein of claim 1, which comprises a polypeptide having an aminoacid sequence: (a) from amino acid 13 to amino acid 43 of SEQ ID NO:1;(b) from amino acid 14 to amino acid 43 of SEQ ID NO:1; (c) from aminoacid 1 to amino acid 49 of SEQ ID NO:1; (d) from amino acid 8 to aminoacid 49 of SEQ ID NO:1; (e) from amino acid 13 to amino acid 49 of SEQID NO:1; (f) from amino acid 14 to amino acid 49 of SEQ ID NO:1; or (g)from amino acid 1 to amino acid 49 of SEQ ID NO:7.
 13. The BAFF-Rglycoprotein of claim 12, which comprises a polypeptide having an aminoacid sequence as set out from amino acid 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, or 19 of SEQ ID NO:1 and to amino acid43, 44, 45, 46, 47, 48, or 49 of SEQ ID NO:1.
 14. The BAFF-Rglycoprotein of claim 12, wherein an amino acid at position 21 of SEQ IDNO:1 is valine and an amino acid at position 28 of SEQ ID NO:1 isleucine.
 15. The BAFF-R glycoprotein of claim 12, wherein an amino acidat position 21 of SEQ ID NO:1 is asparagine and an amino acid atposition 28 of SEQ ID NO:1 is proline.
 16. The BAFF-R glycoprotein ofclaim 12, further comprising at least a portion of an immunoglobulinconstant region, and optionally a linker joining the polypeptide to theportion of the immunoglobulin constant region, wherein the linker doesnot include amino acid 50 to 56 of SEQ ID NO:1. 17-18. (canceled)
 19. Anucleic acid encoding the BAFF-R glycoprotein of claim
 1. 20-21.(canceled)
 22. A vector comprising the nucleic acid of claim
 19. 23. Ahost cell comprising the nucleic acid of claim
 19. 24. A method forproducing the BAFF-R glycoprotein, the method comprising the steps of:(a) transforming host cells with the vector of claim 22; (b) culturingthe host cells under conditions permitting production of the protein;and (c) isolating the BAFF-R glycoprotein from the host cells.
 25. ABAFF-R fusion polypeptide comprising: (a) a first polypeptide comprisingan amino sequence substantially as set out from amino acid 13 to aminoacid 43 or amino acids 14 to 43 of SEQ ID NO:1 fused to (b) a secondamino acid sequence comprising at least a portion of an immunoglobulinconstant region, and optionally (c) a linker joining the first and thesecond sequences, wherein the BAFF-R fusion polypeptide does not includeamino acid 50 to amino acid 56 of SEQ ID NO:1. 26-38. (canceled)
 39. Apharmaceutical composition comprising the BAFF-R glycoprotein ofclaim
 1. 40. A pharmaceutical composition comprising the BAFF-R fusionpolypeptide of claim
 25. 41. A pharmaceutical composition comprising thenucleic acid of claim
 19. 42. A method for treating an immunologicaldisorder comprising administering a therapeutically effective amount ofthe pharmaceutical composition as in any one of claims 39-41 to apatient in need of treatment, thereby treating the immunologicaldisorder. 43-45. (canceled)
 46. A BAFF-R polypeptide comprising aminoacids 14 to 56 of SEQ ID NO:1 having mutations at amino acids 50, 51,and 56 of SEQ ID NO:1, wherein amino acids 50 is not serine orthreonine, amino acid 51 is not serine or threonine, and amino acid 56is not serine or threonine.
 47. The BAFF-R polypeptide of claim 46,further comprising amino acids 14 to 63 of SEQ ID NO:1 and having amutation at amino acid 63 of SEQ ID NO:1 wherein amino acid 63 is notserine or threonine.